Yeovil had failed to complete the signing of Port Vale's Luke Rodgers who had scored in their previous two matches on loan and consequently were weak up front.
They had to wait until stoppage time for their goal which came when substitute Andre McCollin headed in a right-wing corner from Danny Schofield.
Scunthorpe looked the more polished and comfortable side on the ball and it was no great surprise when they took the lead in the 25th minute.
Garry Thompson got to the by-line on the right and pulled the ball back for impressive midfielder Sam Togwell to knock in at close range.
Yeovil's problems increased on 34 minutes when their skipper Terry Skiverton was sent off.
He had joined in with his attack and as he battled for a long ball from Gary Roberts he caught defender Andrew Wright in the face and with blood appearing, referee Dean Whitestone immediately got out his red card.
Yeovil battled on with Aaron Brown coming on in the defence as the Glovers sacrificed striker Gavin Tomlin.
Their attacks were becoming less frequent and it was not a great surprise when the Iron doubled their lead right on half-time.
Gary Hooper chased a long ball from Marcus Williams and out-paced the defence to plant a shot firmly past the left hand of goalkeeper Josh Wagenaar.
Yeovil started the second half in determined fashion and Joe Murphy, in the visitors' goal, had to make his best save of the night in the 47th minute when Schofield got in a powerful header from close range.
It was Yeovil's best effort until the McCollin goal and the Iron were worthy winners.